Changes between Version 4 and Version 5 of MedusaCoupling

Timestamp:

03/15/17 16:42:44 (7 years ago)

Author:

smoreira

Comment:

--

MedusaCoupling

@@ -12 +12 @@
 
 Note: iLOVECLIM - OCYCC uses DIC variable but exchange between MEDUSA and iLOVECLIM is done in terms of HCO,,3,, , CO,,3,, and CO,,2(dis),,
+
 == MEDUSA Description ==
-MEDUSA (Model of Early Diagenesis in the Upper Sediment) is a transient one-dimensional advection-diffusion-reaction model that describes the coupled early diagenesis processes of carbonates and organic matter in the surface sediment.
-Link to the Document of Guy and the papers
+MEDUSA (Model of Early Diagenesis in the Upper Sediment) is a transient one-dimensional advection-diffusion-reaction model that describes the coupled early diagenesis processes of carbonates and organic matter in the surface sediment. MEDUSA sediment model has been developed by Guy Munhoven from the University of Liège (Belgium) < http://www.astro.ulg.ac.be/~munhoven >
+
+In summary,MEDUSA is a transient early diagenesis model originally fully coupled to a multibox model (MBM) of the carbon cycle, as described in Munhoven (2007). This model combines advection, diffusion and reaction processes to describe the early diagenesis processes of organic and inorganic (carbonates) carbon components. Ocean water columns interact directly with a reactive layer and accumulation generates an historical zone. Model includes loopback fluxes to keep a conservative mass balance and emulate riverine and eolian compensation.
 
 == Running a simulation with MEDUSA ==
@@ -24 +26 @@
 * Prepare your restarting files for MEDUSA using reaclay, flx and sedcore files from a previous simulation or, in case you don't want to use any initial condition for MEDUSA, set the corresponding options of medusa_filelist.nml file to "/dev/null"
 
-* Configure your MEDUSA input files and namelists in medusa-svn/inputdata-cpl: medusa.rrp, medusa.tsi, medusa_filelist.nml, medusa_seafloor.init.
+* Configure your MEDUSA input files and namelists in medusa-svn/inputdata-cpl: medusa.rrp, medusa.tsi, medusa_filelist.nml, medusa_seafloor_init.nml
     * It is specially important to pay attention to medusa_filelist.nml, cfn_ncin_sedcore file is the main file for doing a restart in the MEDUSA simulation. In MEDUSA, it is possible to read this input file and create a different output file  cfn_ncout_sedcore file. However, there is a small bug and this option does not work in our current version. Therefore, the procedure suggested is to make a copy of the original sedcore input nectdf file, re-name it and use this file as the same file for input and output (that works perfectly!)
 
@@ -48 +50 @@
 
 
+The other important configuration file is medusa.tsi
+{{{
+
+&nml_timecontrol
+! initial time of the simulation
+ayears_medusaini = 0.0D+00
+! Medusa time step length in days
+ndays_medusastep = 3600
+! Frequency of NetCDF output (every nn Medusa time steps)
+nmedusasteps_ncoutfrequency = 10
+/ 
+
+}}}
+
+which allows to set the number of days of the MEDUSA time step and the frequency of the NETCDF Output
+
+Finally the current default files form medusa.rrp and medusa_seafloor_init.nml are:
+{{{
+&nml_CalcDissolution
+k_1   = 365.25D+00
+n_1   = 4.5D+00
+/
+
+&nml_OrgMatterOxicDegrad
+k_2   = 0.06D+00
+khs_2 = 0.020D+00
+/
+
+}}}
+
+{{{
+! Template for medusa_seafloor_init.nml, automatically generated by
+! CREATE_MOD_SEAFLOOR_INIT from the MEDUSA configuration
+! utility MedusaCoCoGen.
+! Solids'  (prefix "solid_") are expected to be given in %dry-weight
+! Porewater solutes' (prefix "porew_") are expected to be given in mol/m3
+&nml_seafloor_init
+solid_pcent_clay =  100.00D+00
+solid_pcent_calc =    0.00D+00
+porew_molm3_co3 =    81.76D-03
+porew_molm3_hco3 = 2307.01D-03
+porew_molm3_co2 =    31.23D-03
+solid_pcent_om =      0.00D+00
+porew_molm3_o2 =    100.00D-03
+/
+
+}}}
+
 == Coupling description == 
+
+Main aspects of general MEDUSA Coupling are described in detail in ''' MEDUSA-- Guide to Coupling ''' by Guy Munhoven
 Fluxes, loopback fluxes, variables in sediments in the current version.
 Describe the files and modules in the code.